How are points calculated?

Once you achieve a "perfect defense", you increase your score by building fewer towers.

Your score is calculated as follows:

• 1000 points for each core you saved
• 1 point for each dollar left over that you did not spend
• 1 point for each dollar you'd get by selling all towers you built

Since you get less money when you sell a tower than it costs when you buy one, you'll get more points if you never purchase a tower in the first place.

From here:

You can see a summary of how your score was calculated at the end of each level. It's made up of 3 things:

1. The amount of money you have left over
2. The resale value of your towers (how much you would get if you sold them)
3. 1000 points for each core left at the end (24 x 1000 = 24000 if you don't lose any cores)

So to get a higher score you should:

1. Spend the least amount of money possible
2. Use the fewest towers possible and, where possible, use towers with the best resale value
3. Be sure not to lose any cores

It's also good to wait as long as you can before you spend money to build or upgrade because it earns interest until you spend it. Also, try to avoid using the laser because you don't collect resources for aliens that you kill with the laser (the one that shoots from the sky, not the laser tower).

I used to think that the money you had (not spent) counted too, so I also try to sell all my towers when I'm finishing the level.
When you see you're about to kill the last alien, start selling all your towers from places he has already passed and you don't need anymore (reading that post I linked to, I don't think this is true anymore though, I'll have to test it).

In addition to the above tips about how to raise your score, I would add that you can intentionally prolong the end of the level. Because you constantly earn interest on the money you haven't spent, it is best to keep the level going as long as possible after the final aliens have appeared. You can sell some towers to make it take longer to kill the final aliens, and you will earn more interest and thus more points.